Additional file 1 of Methylome and transcriptome analyses of three different degrees of albinism in apple seedlings

Additional file 1: Table S1. Information on the bisulfite sequencing libraries. Table S2. The coverage of the intergenic region. Table S3. The DMRs distributed on each chromosome. Table S4. RNA-seq sequencing data and mapping of the genome. Table S5. Differentially expressed genes involved in the flavonoid, chlorophyll and carotenoid biosynthesis pathways in WM/NL, PM/NL and LM/NL. Table S6. DMR-associated DEGs involved in the carotenoid and flavonoid biosynthesis pathways. Table S7. The average methylation levels in NL, WM, PM and LM. Table S8. The primers used in qRT-PCR and BS-PCR. Fig. S1. Information of the sequencing and mapping. Fig. S2. The global methylome in NL, WM, PM and LM. Fig. S3. The chromosomal mCs distributions in NL, WM, PM and LM. Fig. S4. The KEGG analysis of DMRs in WM/NL, PM/NL and LM/NL. Fig. S5. The principal component analysis (PCA) of expressed genes. Fig. S6. DGEs in WM/NL, PM/NL and LM/NL. Fig. S7. GO and KEGG pathway analyses of the DEGs in WM/NL, PM/NL and LM/NL. Fig. S8. Number of differentially methylated genes of CG, CHG and CHH between DMRs and DEGs in WM/NL, PM/NL and LM/NL. Fig. S9. Relationship between differential methylation and gene expression. Fig. S10. DNA methylation validated in WM/NL, PM/NL and LM/NL. Fig. S11. Gene expression validation involved in the chlorophyll, carotenoid and flavonoid biosynthesis pathways.